A quantum communication system comprising a sending unit and a receiving unit, said sending unit comprising a photon source assembly configured to output a stream of pulses of light having at least two different intensities and a memory configured to store information for determining which pulses should be reference pulses and which pulses should be data pulses, the average intensity of reference pulses being different to the average intensity of data pulses, the receiving unit comprising a memory for storing information for identifying the position of reference pulses within the stream of pulses and a processor for determining the calibration of the quantum communication system from the reference pulses.